Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Behind these supercomputers, experts are helping answer pharma researchers and policymakers’ toughest coronavirus questions.

Exploring the whys, hows and what-ifs of COVID-19 with powerful Intel® technologies.

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change.

Now, scientists and policymakers are turning to these high-performance computing (HPC) systems to help answer some of their most urgent questions about COVID-19 and the novel coronavirus strain that causes it.

“COVID-19 is coming at us from every direction,” says Tim Cockerill, User Services Director at the Texas Advanced Computer Center (TACC) at The University of Texas. “HPC systems are supporting an extraordinarily broad range of research to help us understand the virus and respond to it. HPC is a crucially important part of the research into the coronavirus.”

Models of coronavirus proteins can help in identifying targets for new COVID-19 drug treatments. Image credit: Lorenzo Casalino, Zied Gaieb, Abigail Dommer, Rommie Amaro. UC San Diego.

Which means that behind it all—behind the healthcare heroes delivering critical care, the laboratory scientists seeking cures, and the planners trying to forestall new outbreaks—stand thousands of computational scientists and researchers from around the world who have enlisted in the fight against COVID-19. They’re using the world’s most powerful supercomputers, many based on Intel® processors, to study the virus from every conceivable angle, at scales ranging from the minuscule to the massive.

COVID-19 is coming at us from every direction. HPC systems are supporting an extraordinarily broad range of research to help us understand the virus and respond to it.

Tim Cockerill, User Services Director, Texas Advanced Computer Center

Atom-Level Insights

At the molecular level, research teams are building detailed digital models of the novel coronavirus and running physics-based simulations to explore how it works and what aspects of its molecular structure offer potential targets for vaccines and treatments.

One such team at the University of California San Diego (UCSD) is constructing a complete model of the virus’s exterior shell—the part we’re trying to dissolve when we wash our hands for 20 seconds. They’re also planning to simulate the atom-to-atom interactions of the 200 million atoms that make up the shell.

Researchers are current simulating 300,000 ligands per hour on Frontera. Image credit: Argonne National Laboratory.

The UCSD team runs its codes on the world’s most powerful academic supercomputer1—which resides at TACC and has 8,008 nodes, each as powerful as several desktop computers combined.

A collaboration led by the Department of Energy’s Argonne National Laboratory is using Intel® technologies to scrutinize millions of small molecules, seeking the most promising targets for new drugs to prevent or treat COVID-19.

Both teams share their results with drug developers and other scientists for further explorations.

A Foundation for Science-Based Strategies

At the macro level, scientists and policy analysts want to better understand how COVID-19 is spreading and what containment strategies can best minimize disease transmission and economic disruption. Epidemiological simulations empower them with data for developing science-based answers to these questions.

In one of the largest COVID-19 related epidemiological studies, an 80-person team at the University of Virginia Biocomplexity Institute and partner institutions has built a detailed “digital twin” that models the entire United States population. They use this model to simulate how the U.S. would respond to possible pandemic-related actions, to inform answers to the most pressing “what if” questions. The model runs each night at the Pittsburgh Supercomputing Center, and results are shared with federal and state agencies.

Collaborating to Speed Progress

Supercomputers are so vital to the COVID-19 effort that government, industry, and academic leaders have come together to make sure strategic research initiatives get access to needed resources and expertise. Intel supports researchers as a member of the COVID-19 HPC Consortium, a public-private collaboration initiated by the White House Office of Science and Technology Policy to provide access to HPC resources. Through our ongoing partnerships with HPC centers, research teams, and the open source community, we help optimize performance for critical tools and applications to enable faster progress.

HPC centers are freeing up time on their supercomputers for COVID-related projects. Among others, Germany’s Leibniz Supercomputing Centre and the King Abdullah University of Science and Technology in Saudi Arabia have invited coronavirus-related research teams to apply for time on their Intel® processor-based HPC platforms.

Oil and gas companies have also stepped up. BP is providing cycles on its industrial-scale HPE Apollo supercomputer. Italian oil and gas leader Eni is offering its supercomputing resources and its molecular modeling skills (normally used for seismic research) to help. Eni is working with Dompé, a biopharmaceutical company headquartered in Milan, and Cineca, a nonprofit research consortium, to accelerate the path to COVID-19 treatments.

Fighting COVID-19—and Rising to the Next Global Challenge

Supercomputing is crucial in the fight against COVID-19, and the scientific community has risen to the challenge. Taking advantage of Intel® technologies, scientists are applying their expertise and passion to advance the world’s understanding of the disease, its causes, and its impacts. Industry leaders are collaborating with government agencies and universities to support research initiatives that can help lead to cures and vaccines and provide a basis for data-informed policies.

In doing so, they’re providing a model of how to work together to solve the biggest problems. They’re advancing their algorithms and software in ways that are crucial for understanding COVID-19—and can also help deliver faster, deeper insights into the science behind other global challenges and opportunities.

Armed with this knowledge and experience, we can envision a post-pandemic world that will better prepared to tackle climate change, create smart cities—and face down the next lethal virus that emerges.

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Read more about COVID-19 research projects at the Texas Advanced Computing Center, Argonne National Laboratory, and Pittsburgh Supercomputing Center

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